diff --git a/exercises/phylo_exercise.md b/exercises/phylo_exercise.md index f269edb75e1be0e7c37210e7e2cd0e9c047aa79d..844011e931aafcbd5bcc127e84bc9293c0259fb5 100644 --- a/exercises/phylo_exercise.md +++ b/exercises/phylo_exercise.md @@ -68,7 +68,7 @@ ``` # GENERATE A CORE SNP ALIGNMENT - snippy-core --prefix core [outdir] [outdir2] [outdir3] + snippy-core --prefix core [outdir] [outdir2] [outdir3] --ref [reference] ``` This command will give you various output, but among them is `core.aln` and `core.full.aln`. Both are fasta multiple sequence alignment, the first contains only the core SNPs, the other contains the full alignment of your reference and the samples inlcuding any invariant sites.